ArticleJournal of biomedical semantics2018
OpenBiodiv-O: ontology of the OpenBiodiv knowledge management system.
Article in Journal of biomedical semantics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 54 citations in OpenAlex.
- Ontologies as the semantic bridge between artificial intelligence and healthcare.Frontiers in digital health · 2025Article
- Article
- Wanted: Standards for FAIR taxonomic concept representations and relationships.Biodiversity Information Science and Standards · 2021Article
- Infrastructure and Population of the OpenBiodiv Biodiversity Knowledge Graph.Biodiversity data journal · 2021Article
- Knowledge-Based Biomedical Data Science.Annual review of biomedical data science · 2020Article
- Text-mined fossil biodiversity dynamics using machine learning.Proceedings. Biological sciences · 2019Article
- Verbalizing phylogenomic conflict: Representation of node congruence across competing reconstructions of the neoavian explosion.PLoS computational biology · 2019Article
- Ozymandias: a biodiversity knowledge graph.PeerJ · 2019Article
- Biodiversity Observations Miner: A web application to unlock primary biodiversity data from published literature.Biodiversity data journal · 2019Article
- An updated checklist of the Tenebrionidae sec. Bousquet et al. 2018 of the Algodones Dunes of California, with comments on checklist data practices.Biodiversity data journal · 2018Article
- Liberating links between datasets using lightweight data publishing: an example using plant names and the taxonomic literature.Biodiversity data journal · 2018Article
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Authors and funding
9 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe biodiversity domain, and in particular biological taxonomy, is moving in the direction of semantization of its research outputs. The present work introduces OpenBiodiv-O, the ontology that serves as the basis of the OpenBiodiv Knowledge Management System. Our intent is to provide an ontology that fills the gaps between ontologies for biodiversity resources, such as DarwinCore-based ontologies, and semantic publishing ontologies, such as the SPAR Ontologies. We bridge this gap by providing an ontology focusing on biological taxonomy.
resultsOpenBiodiv-O introduces classes, properties, and axioms in the domains of scholarly biodiversity publishing and biological taxonomy and aligns them with several important domain ontologies (FaBiO, DoCO, DwC, Darwin-SW, NOMEN, ENVO). By doing so, it bridges the ontological gap across scholarly biodiversity publishing and biological taxonomy and allows for the creation of a Linked Open Dataset (LOD) of biodiversity information (a biodiversity knowledge graph) and enables the creation of the OpenBiodiv Knowledge Management System. A key feature of the ontology is that it is an ontology of the scientific process of biological taxonomy and not of any particular state of knowledge. This feature allows it to express a multiplicity of scientific opinions. The resulting OpenBiodiv knowledge system may gain a high level of trust in the scientific community as it does not force a scientific opinion on its users (e.g. practicing taxonomists, library researchers, etc.), but rather provides the tools for experts to encode different views as science progresses.
conclusionsOpenBiodiv-O provides a conceptual model of the structure of a biodiversity publication and the development of related taxonomic concepts. It also serves as the basis for the OpenBiodiv Knowledge Management System.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.